Cluster Analysis of Mycobacterium tuberculosis Using Whole Genome Sequencing (Wgs): The Irish Mycobacteria Reference Laboratory (Imrl) Experience

Tuberculosis (TB) incidence in Ireland, although low at 7/100,000, remains a challenge to Public Health. Genotyping aims to disrupt transmission chains by flagging potential outbreaks. The IMRL performs 24-locus Mycobacterial-Interspersed-Repetitive-Unit Variable-NumberTandem-Repeat (MIRU-VNTR) genotyping. However, WGS could be the ultimate genotyping tool as it surveys the entire genome. In this study, Illumina Next-Generation-Sequencing was used to further investigate MIRU-VNTR clusters to discover whether WGS confirms or outrules them as outbreaks. Ten clusters were chosen from the IMRL national collection over the period 2006-14. The largest of these was Cluster 10 from an institutional outbreak (n=25) followed by Cluster 1 (n=23). Cluster 2 contained two sub-clusters (a, n=21 and b, n=20) that differed by a single locus variation (SLV). Seven smaller clusters were also included. Isolates were grown in liquid culture followed by WGS, using published protocols. Fastq files were analysed using a pipeline developed by the Modernising Medical Microbiology Group (Stampy, BWA, Samtools and PhyML form part of a custom pipeline). Phylogenetic trees were visualised using freely available software. The Public Health Department collected linked epidemiological data. Cluster 10 sequences differed by less than 4 single nucleotide variations (SNVs) confirming a single strain outbreak and raising the possibility of a ‘super-spreader’. Cluster 2 was identified as a single strain outbreak (n=41). Cluster 6 isolates differed by at least 60 SNVs, which rules out recent transmission. All six patients in this cluster shared the same country of origin indicating that their isolates are probably from a common ancestor. Our results show that WGS can both rule-in and rule-out outbreaks with greater discrimination than MIRU-VNTR genotyping and can confirm recent transmission events, making it a valuable tool in the fight against TB.